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Glycine has a dipole moment, so why is it considered a nonpolar amino acid when discussing its occurrence in proteins?

Also, is the backbone of a protein nonpolar?

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    $\begingroup$ @AlwaysConfused please read the text that appears when you start to write a new comment - "Use comments to ask for more information or suggest improvements. Avoid answering questions in comments." You have been doing this a lot lately. Please stop. $\endgroup$ – MattDMo Nov 27 '16 at 19:03
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    $\begingroup$ @MattDMo On many cases users (including moderators) put brief/ simplified answer in comment. Such as this comment by you ( permalink ) tells "Of course they do. If you take away a substance that is killing certain cells, of course the number of those cells will increase. I don't understand how that has anything to do with HIV infection and CD4 levels. –" ; which is an answer to a question. $\endgroup$ – Always Confused Nov 28 '16 at 7:56
  • $\begingroup$ As well, when it is not possible to write immediately an elaborate answer by an user, a small hint to the answer could greatly help the asker. $\endgroup$ – Always Confused Nov 28 '16 at 8:01
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    $\begingroup$ @AlwaysConfused That's fine for a short hint but your comments just get too long, spanning two or three comment boxes. If you have time for such a long comment then better give an answer. $\endgroup$ – WYSIWYG Nov 28 '16 at 8:23
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    $\begingroup$ @AlwaysConfused Please take heed of MattDMo's comment. StackExchange has a particular model for particular reasons. If you answer in a comment you break this model. The question is marked as unanswered and there is no way for anyone to up- or down-vote your comment/answer so that other readers can get a feel of whether the answer is likely to be correct. I feel very strongly about this and have made my views clear in an answer to meta.english.stackexchange.com/questions/2653/… $\endgroup$ – David Nov 28 '16 at 14:03
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The first part of your question illustrates a common confusion of beginners between the physiochemical properties of free amino acids in solution, and the properties of that part of an amino acid that remains after it has participated in a condensation reaction to form part of a polypeptide. They are different. (It was for that reason that I modified the question to make it clear that the ‘consideration’ of glycine as nonpolar applies to it in its protein context.)

I have prepared a diagram to clarify.

  • As can be seen on line 1, all free amino acids at physiological pH are charged because of the pKa of the α-amino and α-carboxyl groups (proline, as an imino acid is the exception). The chemical features common to all amino acids are shown in blue, for the second amino acid, and the unique feature — wherein amino acids differ — is shown in red.
  • To show amino acid 2 in the context of a polypeptide chain, I have condensed it with two other amino acids (1 and 3) to produce a tripeptide (line 3). (This is the situation most amino acids in a long polypeptide chain will be in, as there are only two that will be at the ends.)
  • You can see from the colouring that what is left of the amino acid in the protein — the amino acid residue — has lost the charges of the α-amino and α-carboxyl groups, which have become parts of peptide bonds. (A molecule of water is removed in a condensation.)
  • The properties that a particular amino acid endows to a protein are those of the ‘R-group’— R2 in the diagram. In the case of glycine, R is H, so that in the context of proteins we regard glycine as a non-polar amino acid (The C-H bond has a negligible dipole.)
  • Don’t confuse R with residue. It is a side-chain, designated using a common chemical abbreviation. What remains after an amino acid is condensed into a protein

The second question was “is the backbone of the macromolecule nonpolar?”.

No. The backbone of a protein has partial charges on the oxygen and nitrogen atoms of the peptide bond, as shown below. This is because it has a partial double-bonded character. These partially charged atoms can (and frequently do) form hydgrogen bonds, either with another part of the backbone (secondary structure such as α-helix or β-sheet) or with polar side-chains.

Peptide bond charge

Reading

Berg et al. Section 3.2 covers the basics (although it fails to emphasize the difference in properties of amino acids and amino acid residues) and Section 3.3 covers the role of the peptide bond in protein secondary structure.

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I'm just converting @alwaysconfused's comment into answer (with a bit of more details).

Yes, glycine does have a dipole moment (15.7 D), but when it comes to biochemistry, then the dipole moment on the side chain is considered. Since the structure of glycine is:

H2N - CH2 - COOH <---> H3N+ - CH2 - COO-

So the side chain is:

-H-

which has, obviously, 0 dipole moment. Thus glycine, though polar, is considered non-polar in protein structures.

Source

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Glycine has no side chains. In a neutral solution; not forming a peptide bond, glycine has the following the following structure

H3N+ - CH3 - COO-

which is polar because of the -ve and +ve charge. Once it forms a peptide bond with another aminoacids (aa), it becomes in the following form:

aa-----H2N - CH2 - CO ------aa

As you can see, it doesn't have any charges on it since the amino group and the carboxylic acid group formed bonds with another 2 amino acids.

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    $\begingroup$ I just upvoted your answer, but there is a mistake: every AA has a dude chain. The side chain of glycine, btw, is the simplest possible in chemistry: H. $\endgroup$ – user24284 Dec 7 '16 at 8:33
  • $\begingroup$ @David: Pentavalent carbon corrected. $\endgroup$ – Mohamed Nasef Dec 8 '16 at 14:48

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